Software Skills for Scientists and Engineers

General Information

Software Carpentry's mission
is to help people become more productive
by teaching them basic computing skills
like program design, version control, data management, and task automation.
This two-day hands-on workshop will cover basic concepts and tools;
participants will be encouraged to help one another
and to apply what they have learned to their own research problems.
Note that the workshop is open to everyone, not just PyCon attendees.

Setup

To participate in a Software Carpentry bootcamp,
you will need working copies of the software described below.
Please make sure to install everything
(or at least to download the installers)
before the start of your bootcamp.

Overview

Editor

When you're writing code, it's nice to have a text
editor that is optimized for writing code, with features
like automatic color-coding of key words.
The default text editor on Mac OS X and Linux is usually set to Vim,
which is not famous for being intuitive.
if you accidentally find yourself stuck in it,
try typing the escape key,
followed by ':q!' (colon, lower-case 'q', exclamation mark),
then hitting Return
to return to the shell.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you
more power to do more tasks more quickly with your
computer.

Git

Git is a state-of-the-art version control system. It
lets you track who made changes to what when and has
options for easily updating a shared or public version of
your code on github.com.

Python

Python is becoming very popular in scientific computing,
and it's a great language for teaching general programming concepts due to its easy-to-read syntax.
We teach with Python version 2.7,
since it is still the most widely used.
Installing all the scientific packages for Python individually can be a bit difficult,
so we recommend an all-in-one installer.

SQL

SQL is a specialized programming language used with databases.
We use a simple database manager called SQLite,
either directly or through a browser plugin.

Windows

Software Carpentry Installer

If the file opens directly in the browser select File→Save Page As
to download it to your computer.

Double click on the file to run it.

Editor

Notepad++ is a
popular free code editor for Windows.
Be aware that you must add its installation directory to your system path
in order to launch it from the command line
(or have other tools like Git launch it for you).
Please ask your instructor to help you do this.

Git Bash

Install Git for Windows by download and running
the installer.
This will provide you with both Git and Bash in the Git Bash program.

Python

Use all of the defaults for installation
except
make sure to check Make Anaconda the default Python.

SQLite

Download the sqlite3 program
and put it in the directory where you are running examples.
Alternatively,
you may install the Firefox SQLite browser plugin described below.

Mac OS X

Bash

The default shell in all versions of Mac OS X is bash,
so no need to install anything. You access bash from
the Terminal (found
in /Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.

SQLite

Linux

Bash

The default shell is usually bash,
but if your machine is set up differently
you can run it by opening a terminal and typing bash.
There is no need to install anything.

Git

If Git is not already available on your machine you can try
to install it via your distro's package manager
(e.g. apt-get).

Editor

Kate is one option for Linux users.
In a pinch, you can use nano,
which should be pre-installed.

SQLite

sqlite3 comes pre-installed on Linux.
Alternatively,
you may install the Firefox SQLite browser plugin described below.

Python

We recommend the all-in-one scientific Python installer
Anaconda.
(Installation requires using the shell and if you aren't
comfortable doing the installation yourself just
download the installer and we'll help you at the boot
camp.)

Download the installer that matches your operating
system and save it in your home folder.

Open a terminal window.

Type

bash Anaconda-

and then press
tab. The name of the file you just downloaded should
appear.

Press enter. You will follow the text-only
prompts. When there is a colon at the bottom of the
screen press the down arrow to move down through the
text. Type yes and press enter to approve
the license. Press enter to approve the default
location for the files. Type yes and
press enter to prepend Anaconda to
your PATH (this makes the Anaconda
distribution the default Python).